Kate Culhane, Dept. of Ecology, Evolution, and Marine Biology, UC Santa Barbara
kathrynculhane@ucsb.edu


Summary

Exploring the data


DEPENDENCIES

##### PACKAGES #####

library(tidyverse) # data manipulation & visualization
library(vegan) # community analyses
library(goeveg) # scree plot for NMDS

##### DATA #####

# Invertebrate counts by order from sticky and pitfall trap samples
prey <- read_csv("output/02_prey.csv")

# Invertebrate counts by order from lizard stomach pumping samples
diet <- read_csv("output/02_diet_inverts.csv")

# Site by species matrix (invert prey data)
prey_matrix <- read_csv("output/02_prey_matrix.csv")

# Site by species matrix (diet data)
diet_matrix <- read_csv("output/02_diet_matrix.csv")

Abundance by order

Available prey community

# Summary table
prey %>% 
  group_by(order, trap_type) %>% 
  summarise(n = sum(count)) %>% 
  pivot_wider(names_from = trap_type, values_from = n) %>% 
  mutate(total = pitfall + sticky) %>% 
  arrange(-total)
# Abundance by order
prey %>% 
  ggplot(aes(x = trap_type, y = count)) +
  geom_jitter(aes(color = trap_type),
              width = 0.1, size = 1.5) +
  geom_boxplot(fill = NA, outlier.shape = NA) +
  facet_wrap(~ fct_reorder(order, count, .fun = sum, .desc = TRUE),
             scales = "free_y") +
  theme_classic() +
  theme(legend.position = "NA") +
  labs(x = "Trap type", y = "Abundance (indv/trap)")

Diet

# Summary table
diet %>% 
  group_by(order) %>% 
  summarise(n = sum(count)) %>% 
  arrange(-n)
# Abundance by order
diet %>% 
  # Data wrangling
  group_by(order) %>% 
  mutate(n = length(count)) %>% 
  # Plot
  ggplot(aes(x = fct_reorder(order, count, .fun = sum, .desc = TRUE), y = count)) +
  geom_jitter(width = 0.1, size = 1.5) +
  geom_boxplot(fill = NA, outlier.shape = NA) +
  geom_text(aes(y = 80, label = paste("n =", n)),
            stat = "unique", angle = 90, size = 3) +
  scale_y_log10() +
  theme_classic() +
  theme(legend.position = "NA",
        axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)) +
  labs(x = "Order", y = "Abundance (indv/lizard)")

NMDS

Invert trap data

# Wrangle matrix
m_p <- as.matrix(prey_matrix[-c(1:4)])
rownames(m_p) <- prey_matrix$sample
m_p_hell <- decostand(m_p, 'hellinger') # Hellinger transformation
m_p_meta <- select(prey_matrix, sample, site, trap, trap_type) # metadata

# Scree plot to check stress per number of dimensions
dimcheckMDS(m_p_hell, distance = "bray", autotransform = FALSE, k = 10)

# Create NMDS ordination
ord <- metaMDS(m_p_hell,
               distance = 'bray', # use Bray-Curtis distances
               autotransform = FALSE, # already manually transformed the matrix
               k = 3, # number of dimensions
               trymax = 1000)

# Stress plot
stressplot(ord)

## Run 0 stress 0.2455473 
## Run 1 stress 0.2232751 
## ... New best solution
## ... Procrustes: rmse 0.01714159  max resid 0.1989876 
## Run 2 stress 0.2299027 
## Run 3 stress 0.4715637 
## Run 4 stress 0.2402168 
## Run 5 stress 0.2231786 
## ... New best solution
## ... Procrustes: rmse 0.002964788  max resid 0.02966872 
## Run 6 stress 0.2362589 
## Run 7 stress 0.2232164 
## ... Procrustes: rmse 0.00430651  max resid 0.04670683 
## Run 8 stress 0.2227869 
## ... New best solution
## ... Procrustes: rmse 0.005050154  max resid 0.06800828 
## Run 9 stress 0.222782 
## ... New best solution
## ... Procrustes: rmse 0.0003702364  max resid 0.002786871 
## ... Similar to previous best
## Run 10 stress 0.2230862 
## ... Procrustes: rmse 0.005521183  max resid 0.06134435 
## Run 11 stress 0.2414472 
## Run 12 stress 0.2295934 
## Run 13 stress 0.2230211 
## ... Procrustes: rmse 0.005498272  max resid 0.06124748 
## Run 14 stress 0.4730423 
## Run 15 stress 0.4721186 
## Run 16 stress 0.2377542 
## Run 17 stress 0.2228147 
## ... Procrustes: rmse 0.003233775  max resid 0.04351447 
## Run 18 stress 0.2231378 
## ... Procrustes: rmse 0.004597609  max resid 0.06113926 
## Run 19 stress 0.2287039 
## Run 20 stress 0.2297875 
## *** Solution reached
## Run 0 stress 0.1436293 
## Run 1 stress 0.1486094 
## Run 2 stress 0.1443403 
## Run 3 stress 0.1442081 
## Run 4 stress 0.1531921 
## Run 5 stress 0.1502679 
## Run 6 stress 0.1612787 
## Run 7 stress 0.1566424 
## Run 8 stress 0.1570929 
## Run 9 stress 0.1486384 
## Run 10 stress 0.1535379 
## Run 11 stress 0.159447 
## Run 12 stress 0.1464486 
## Run 13 stress 0.1544913 
## Run 14 stress 0.1461988 
## Run 15 stress 0.1576453 
## Run 16 stress 0.1496064 
## Run 17 stress 0.1564018 
## Run 18 stress 0.1480887 
## Run 19 stress 0.1493734 
## Run 20 stress 0.1494265 
## *** No convergence -- monoMDS stopping criteria:
##     18: stress ratio > sratmax
##      2: scale factor of the gradient < sfgrmin
## Run 0 stress 0.09709427 
## Run 1 stress 0.09754663 
## ... Procrustes: rmse 0.01026544  max resid 0.09711669 
## Run 2 stress 0.09747948 
## ... Procrustes: rmse 0.009486836  max resid 0.1245058 
## Run 3 stress 0.09754762 
## ... Procrustes: rmse 0.01036333  max resid 0.09739683 
## Run 4 stress 0.09709435 
## ... Procrustes: rmse 0.0001189573  max resid 0.0008117857 
## ... Similar to previous best
## Run 5 stress 0.0975505 
## ... Procrustes: rmse 0.0101535  max resid 0.09699696 
## Run 6 stress 0.0973508 
## ... Procrustes: rmse 0.009563138  max resid 0.09722738 
## Run 7 stress 0.0974769 
## ... Procrustes: rmse 0.00934962  max resid 0.1239022 
## Run 8 stress 0.09755259 
## ... Procrustes: rmse 0.01017122  max resid 0.09697986 
## Run 9 stress 0.09767318 
## Run 10 stress 0.09744191 
## ... Procrustes: rmse 0.009506244  max resid 0.09224772 
## Run 11 stress 0.09727104 
## ... Procrustes: rmse 0.004930243  max resid 0.05705233 
## Run 12 stress 0.09765486 
## Run 13 stress 0.09765213 
## Run 14 stress 0.09771143 
## Run 15 stress 0.0972685 
## ... Procrustes: rmse 0.004958955  max resid 0.0576244 
## Run 16 stress 0.09822962 
## Run 17 stress 0.09705864 
## ... New best solution
## ... Procrustes: rmse 0.002956479  max resid 0.0400573 
## Run 18 stress 0.09709413 
## ... Procrustes: rmse 0.002939072  max resid 0.03999258 
## Run 19 stress 0.09762706 
## Run 20 stress 0.09709425 
## ... Procrustes: rmse 0.00293682  max resid 0.04000608 
## *** No convergence -- monoMDS stopping criteria:
##      6: no. of iterations >= maxit
##     12: stress ratio > sratmax
##      2: scale factor of the gradient < sfgrmin
## Run 0 stress 0.07047178 
## Run 1 stress 0.07102312 
## Run 2 stress 0.07110785 
## Run 3 stress 0.0714534 
## Run 4 stress 0.07086136 
## ... Procrustes: rmse 0.006679332  max resid 0.06491642 
## Run 5 stress 0.07039018 
## ... New best solution
## ... Procrustes: rmse 0.003502336  max resid 0.03262194 
## Run 6 stress 0.07038655 
## ... New best solution
## ... Procrustes: rmse 0.0008773334  max resid 0.01070979 
## Run 7 stress 0.07025201 
## ... New best solution
## ... Procrustes: rmse 0.004648263  max resid 0.06547353 
## Run 8 stress 0.07026352 
## ... Procrustes: rmse 0.001136088  max resid 0.00953059 
## ... Similar to previous best
## Run 9 stress 0.07027176 
## ... Procrustes: rmse 0.002038886  max resid 0.02091927 
## Run 10 stress 0.07101319 
## Run 11 stress 0.0702583 
## ... Procrustes: rmse 0.0003942782  max resid 0.003288427 
## ... Similar to previous best
## Run 12 stress 0.07101966 
## Run 13 stress 0.07025307 
## ... Procrustes: rmse 0.0008700268  max resid 0.008826028 
## ... Similar to previous best
## Run 14 stress 0.0702645 
## ... Procrustes: rmse 0.001500786  max resid 0.01063863 
## Run 15 stress 0.07044296 
## ... Procrustes: rmse 0.006090172  max resid 0.06699288 
## Run 16 stress 0.07156488 
## Run 17 stress 0.07116915 
## Run 18 stress 0.07040376 
## ... Procrustes: rmse 0.003543406  max resid 0.03344676 
## Run 19 stress 0.0714708 
## Run 20 stress 0.07105251 
## *** Solution reached
## Run 0 stress 0.05433226 
## Run 1 stress 0.05440777 
## ... Procrustes: rmse 0.009616066  max resid 0.09068029 
## Run 2 stress 0.0551087 
## Run 3 stress 0.05506838 
## Run 4 stress 0.05435078 
## ... Procrustes: rmse 0.001966295  max resid 0.01177023 
## Run 5 stress 0.05450461 
## ... Procrustes: rmse 0.00752855  max resid 0.07160852 
## Run 6 stress 0.05441785 
## ... Procrustes: rmse 0.006554141  max resid 0.08895075 
## Run 7 stress 0.05440365 
## ... Procrustes: rmse 0.009338949  max resid 0.08697532 
## Run 8 stress 0.0544859 
## ... Procrustes: rmse 0.01612902  max resid 0.08247204 
## Run 9 stress 0.05444043 
## ... Procrustes: rmse 0.008025015  max resid 0.08414216 
## Run 10 stress 0.05448708 
## ... Procrustes: rmse 0.01598595  max resid 0.08083864 
## Run 11 stress 0.05440275 
## ... Procrustes: rmse 0.01694273  max resid 0.09308145 
## Run 12 stress 0.05482016 
## ... Procrustes: rmse 0.01635894  max resid 0.08640639 
## Run 13 stress 0.05433185 
## ... New best solution
## ... Procrustes: rmse 0.001086522  max resid 0.007105274 
## ... Similar to previous best
## Run 14 stress 0.05441251 
## ... Procrustes: rmse 0.01663053  max resid 0.09510967 
## Run 15 stress 0.05449811 
## ... Procrustes: rmse 0.01544921  max resid 0.07965806 
## Run 16 stress 0.05447836 
## ... Procrustes: rmse 0.005970604  max resid 0.05415409 
## Run 17 stress 0.05448382 
## ... Procrustes: rmse 0.01568316  max resid 0.08021311 
## Run 18 stress 0.05444392 
## ... Procrustes: rmse 0.007005956  max resid 0.08447444 
## Run 19 stress 0.05439602 
## ... Procrustes: rmse 0.005099943  max resid 0.05931647 
## Run 20 stress 0.05440373 
## ... Procrustes: rmse 0.009240614  max resid 0.08775656 
## *** Solution reached
## Run 0 stress 0.04561447 
## Run 1 stress 0.04591376 
## ... Procrustes: rmse 0.01185613  max resid 0.09519358 
## Run 2 stress 0.0456304 
## ... Procrustes: rmse 0.008583637  max resid 0.09847771 
## Run 3 stress 0.04581267 
## ... Procrustes: rmse 0.005996179  max resid 0.04583005 
## Run 4 stress 0.04625355 
## Run 5 stress 0.04557202 
## ... New best solution
## ... Procrustes: rmse 0.007123406  max resid 0.09781215 
## Run 6 stress 0.04627167 
## Run 7 stress 0.04571769 
## ... Procrustes: rmse 0.008947837  max resid 0.0918862 
## Run 8 stress 0.04612425 
## Run 9 stress 0.04640134 
## Run 10 stress 0.04650936 
## Run 11 stress 0.04559427 
## ... Procrustes: rmse 0.002769385  max resid 0.02483894 
## Run 12 stress 0.04572434 
## ... Procrustes: rmse 0.008604123  max resid 0.09044336 
## Run 13 stress 0.04615068 
## Run 14 stress 0.04588088 
## ... Procrustes: rmse 0.01125041  max resid 0.09493494 
## Run 15 stress 0.04563303 
## ... Procrustes: rmse 0.003525593  max resid 0.02701594 
## Run 16 stress 0.04584846 
## ... Procrustes: rmse 0.008917234  max resid 0.07743574 
## Run 17 stress 0.04556203 
## ... New best solution
## ... Procrustes: rmse 0.00156025  max resid 0.009410429 
## ... Similar to previous best
## Run 18 stress 0.04647915 
## Run 19 stress 0.04563358 
## ... Procrustes: rmse 0.002864333  max resid 0.01316102 
## Run 20 stress 0.04583206 
## ... Procrustes: rmse 0.01389679  max resid 0.09638363 
## *** Solution reached
## Run 0 stress 0.03951312 
## Run 1 stress 0.03955809 
## ... Procrustes: rmse 0.003166683  max resid 0.01377554 
## Run 2 stress 0.04097779 
## Run 3 stress 0.04018418 
## Run 4 stress 0.04007966 
## Run 5 stress 0.04085249 
## Run 6 stress 0.04076794 
## Run 7 stress 0.04001254 
## ... Procrustes: rmse 0.01071903  max resid 0.05097976 
## Run 8 stress 0.04072747 
## Run 9 stress 0.04052628 
## Run 10 stress 0.04093845 
## Run 11 stress 0.03967428 
## ... Procrustes: rmse 0.006655434  max resid 0.03328485 
## Run 12 stress 0.04076596 
## Run 13 stress 0.03970225 
## ... Procrustes: rmse 0.006581284  max resid 0.07138278 
## Run 14 stress 0.03973123 
## ... Procrustes: rmse 0.00457872  max resid 0.02005867 
## Run 15 stress 0.04058963 
## Run 16 stress 0.04019474 
## Run 17 stress 0.03988703 
## ... Procrustes: rmse 0.007349436  max resid 0.04051853 
## Run 18 stress 0.04104897 
## Run 19 stress 0.03954788 
## ... Procrustes: rmse 0.008420895  max resid 0.1037123 
## Run 20 stress 0.04018163 
## *** No convergence -- monoMDS stopping criteria:
##     20: no. of iterations >= maxit
## Run 0 stress 0.03474612 
## Run 1 stress 0.03582044 
## Run 2 stress 0.03498145 
## ... Procrustes: rmse 0.0081422  max resid 0.06983254 
## Run 3 stress 0.03495153 
## ... Procrustes: rmse 0.009618641  max resid 0.1049364 
## Run 4 stress 0.03590216 
## Run 5 stress 0.0363347 
## Run 6 stress 0.03494025 
## ... Procrustes: rmse 0.01418837  max resid 0.1056096 
## Run 7 stress 0.03532195 
## Run 8 stress 0.03560952 
## Run 9 stress 0.0356108 
## Run 10 stress 0.03531885 
## Run 11 stress 0.03540635 
## Run 12 stress 0.03516325 
## ... Procrustes: rmse 0.01061268  max resid 0.1081029 
## Run 13 stress 0.03529965 
## Run 14 stress 0.03558062 
## Run 15 stress 0.03524526 
## ... Procrustes: rmse 0.008307538  max resid 0.04248 
## Run 16 stress 0.03528605 
## Run 17 stress 0.03498036 
## ... Procrustes: rmse 0.006324409  max resid 0.03143328 
## Run 18 stress 0.03500067 
## ... Procrustes: rmse 0.007852123  max resid 0.04148387 
## Run 19 stress 0.03509831 
## ... Procrustes: rmse 0.01018218  max resid 0.09295522 
## Run 20 stress 0.0349813 
## ... Procrustes: rmse 0.006623939  max resid 0.04036651 
## *** No convergence -- monoMDS stopping criteria:
##     20: no. of iterations >= maxit
## Run 0 stress 0.03098824 
## Run 1 stress 0.03090659 
## ... New best solution
## ... Procrustes: rmse 0.006674616  max resid 0.04173228 
## Run 2 stress 0.03146113 
## Run 3 stress 0.03119189 
## ... Procrustes: rmse 0.01481912  max resid 0.08172965 
## Run 4 stress 0.03192555 
## Run 5 stress 0.03135098 
## ... Procrustes: rmse 0.01413882  max resid 0.04802066 
## Run 6 stress 0.03117608 
## ... Procrustes: rmse 0.009615589  max resid 0.07672595 
## Run 7 stress 0.03125503 
## ... Procrustes: rmse 0.01427534  max resid 0.0591329 
## Run 8 stress 0.03126717 
## ... Procrustes: rmse 0.01470226  max resid 0.07015532 
## Run 9 stress 0.03150747 
## Run 10 stress 0.03155611 
## Run 11 stress 0.03115034 
## ... Procrustes: rmse 0.007648187  max resid 0.04033101 
## Run 12 stress 0.03125622 
## ... Procrustes: rmse 0.01157045  max resid 0.05370108 
## Run 13 stress 0.03100039 
## ... Procrustes: rmse 0.01329824  max resid 0.06402712 
## Run 14 stress 0.03187234 
## Run 15 stress 0.03155899 
## Run 16 stress 0.03148414 
## Run 17 stress 0.03159434 
## Run 18 stress 0.03216149 
## Run 19 stress 0.0311361 
## ... Procrustes: rmse 0.01315832  max resid 0.1090221 
## Run 20 stress 0.03123222 
## ... Procrustes: rmse 0.01433109  max resid 0.06351897 
## *** No convergence -- monoMDS stopping criteria:
##     20: no. of iterations >= maxit
## Run 0 stress 0.02752796 
## Run 1 stress 0.02846168 
## Run 2 stress 0.02825818 
## Run 3 stress 0.02828048 
## Run 4 stress 0.0279855 
## ... Procrustes: rmse 0.01570628  max resid 0.07782326 
## Run 5 stress 0.02815047 
## Run 6 stress 0.02840748 
## Run 7 stress 0.02813255 
## Run 8 stress 0.02833736 
## Run 9 stress 0.02812444 
## Run 10 stress 0.02816788 
## Run 11 stress 0.02803591 
## Run 12 stress 0.02787408 
## ... Procrustes: rmse 0.01160137  max resid 0.07454286 
## Run 13 stress 0.02812524 
## Run 14 stress 0.0280183 
## ... Procrustes: rmse 0.01227147  max resid 0.07013725 
## Run 15 stress 0.02825886 
## Run 16 stress 0.02857985 
## Run 17 stress 0.02856852 
## Run 18 stress 0.02804476 
## Run 19 stress 0.02790595 
## ... Procrustes: rmse 0.009173516  max resid 0.05111299 
## Run 20 stress 0.0283807 
## *** No convergence -- monoMDS stopping criteria:
##     20: no. of iterations >= maxit
##  [1] 0.22278198 0.14362935 0.09705864 0.07025201 0.05433185 0.04556203 0.03951312 0.03474612 0.03090659
## [10] 0.02752796
## Run 0 stress 0.09709427 
## Run 1 stress 0.09752464 
## ... Procrustes: rmse 0.01008714  max resid 0.1271265 
## Run 2 stress 0.09705968 
## ... New best solution
## ... Procrustes: rmse 0.00295956  max resid 0.04002841 
## Run 3 stress 0.09790286 
## Run 4 stress 0.09764614 
## Run 5 stress 0.09754717 
## ... Procrustes: rmse 0.009416431  max resid 0.09708316 
## Run 6 stress 0.09744272 
## ... Procrustes: rmse 0.008364005  max resid 0.09190001 
## Run 7 stress 0.09735173 
## ... Procrustes: rmse 0.008519178  max resid 0.09689312 
## Run 8 stress 0.09999102 
## Run 9 stress 0.09730257 
## ... Procrustes: rmse 0.004945427  max resid 0.05715123 
## Run 10 stress 0.1030611 
## Run 11 stress 0.0973513 
## ... Procrustes: rmse 0.008480727  max resid 0.09678826 
## Run 12 stress 0.09744229 
## ... Procrustes: rmse 0.008507725  max resid 0.09253177 
## Run 13 stress 0.09744197 
## ... Procrustes: rmse 0.008521106  max resid 0.09255885 
## Run 14 stress 0.09762664 
## Run 15 stress 0.09747689 
## ... Procrustes: rmse 0.01018135  max resid 0.1252437 
## Run 16 stress 0.0975473 
## ... Procrustes: rmse 0.009412099  max resid 0.09706666 
## Run 17 stress 0.09709419 
## ... Procrustes: rmse 0.002960429  max resid 0.04005042 
## Run 18 stress 0.09726846 
## ... Procrustes: rmse 0.00399885  max resid 0.05747728 
## Run 19 stress 0.09764679 
## Run 20 stress 0.09754703 
## ... Procrustes: rmse 0.009356695  max resid 0.09694469 
## Run 21 stress 0.09812755 
## Run 22 stress 0.09735093 
## ... Procrustes: rmse 0.008465  max resid 0.09679764 
## Run 23 stress 0.09793137 
## Run 24 stress 0.09709429 
## ... Procrustes: rmse 0.002980367  max resid 0.04018898 
## Run 25 stress 0.1030722 
## Run 26 stress 0.0973506 
## ... Procrustes: rmse 0.008476784  max resid 0.09681038 
## Run 27 stress 0.09735836 
## ... Procrustes: rmse 0.008726471  max resid 0.0973588 
## Run 28 stress 0.09709419 
## ... Procrustes: rmse 0.002942892  max resid 0.03993169 
## Run 29 stress 0.09730249 
## ... Procrustes: rmse 0.004965041  max resid 0.05737245 
## Run 30 stress 0.09747798 
## ... Procrustes: rmse 0.01030636  max resid 0.1260115 
## Run 31 stress 0.1036483 
## Run 32 stress 0.09785358 
## Run 33 stress 0.09754711 
## ... Procrustes: rmse 0.009371423  max resid 0.09692902 
## Run 34 stress 0.09709413 
## ... Procrustes: rmse 0.002955177  max resid 0.0400403 
## Run 35 stress 0.0976721 
## Run 36 stress 0.09755285 
## ... Procrustes: rmse 0.009127096  max resid 0.09643863 
## Run 37 stress 0.09709445 
## ... Procrustes: rmse 0.002961864  max resid 0.04000355 
## Run 38 stress 0.09744179 
## ... Procrustes: rmse 0.008477265  max resid 0.09237306 
## Run 39 stress 0.09735091 
## ... Procrustes: rmse 0.008520017  max resid 0.09688551 
## Run 40 stress 0.0976762 
## Run 41 stress 0.09953752 
## Run 42 stress 0.09759276 
## Run 43 stress 0.09754511 
## ... Procrustes: rmse 0.01117335  max resid 0.1293348 
## Run 44 stress 0.0974427 
## ... Procrustes: rmse 0.008428997  max resid 0.09208082 
## Run 45 stress 0.09709408 
## ... Procrustes: rmse 0.002941022  max resid 0.03993722 
## Run 46 stress 0.09762782 
## Run 47 stress 0.09709437 
## ... Procrustes: rmse 0.002940994  max resid 0.039895 
## Run 48 stress 0.09736839 
## ... Procrustes: rmse 0.008017193  max resid 0.09617392 
## Run 49 stress 0.09990943 
## Run 50 stress 0.09988678 
## Run 51 stress 0.09730263 
## ... Procrustes: rmse 0.004947315  max resid 0.05709419 
## Run 52 stress 0.09744247 
## ... Procrustes: rmse 0.008511408  max resid 0.09252669 
## Run 53 stress 0.09859683 
## Run 54 stress 0.09709454 
## ... Procrustes: rmse 0.002949577  max resid 0.03993896 
## Run 55 stress 0.09754722 
## ... Procrustes: rmse 0.009329974  max resid 0.09699089 
## Run 56 stress 0.09765502 
## Run 57 stress 0.1031211 
## Run 58 stress 0.09762715 
## Run 59 stress 0.09735224 
## ... Procrustes: rmse 0.008374446  max resid 0.09653822 
## Run 60 stress 0.09765229 
## Run 61 stress 0.1017665 
## Run 62 stress 0.1059232 
## Run 63 stress 0.09778261 
## Run 64 stress 0.0976887 
## Run 65 stress 0.09747787 
## ... Procrustes: rmse 0.01021409  max resid 0.125621 
## Run 66 stress 0.09740409 
## ... Procrustes: rmse 0.007518059  max resid 0.0958859 
## Run 67 stress 0.09868929 
## Run 68 stress 0.09771011 
## Run 69 stress 0.09706021 
## ... Procrustes: rmse 0.0001494077  max resid 0.001793836 
## ... Similar to previous best
## *** Solution reached
# Plot ordination
scale_trap <- c("red", "orange")
names(scale_trap) <- c("pitfall", "sticky")
par(mar = c(4,4,1,1))
plot(ord, display = 'species', type = 'n')
points(ord, display = 'sites', pch = 19, col = scale_trap[m_p_meta$trap_type])
ordiellipse(ord, groups = m_p_meta$trap_type,
            label = TRUE, col = scale_trap, lwd = 2)
text(ord, display = 'species')

Ordination stress = 0.0970597

Notes & resources




Session info
devtools::session_info()
## - Session info ------------------------------------------------------------------------------------------
##  setting  value                       
##  version  R version 4.1.0 (2021-05-18)
##  os       Windows 10 x64              
##  system   i386, mingw32               
##  ui       RStudio                     
##  language (EN)                        
##  collate  English_United States.1252  
##  ctype    English_United States.1252  
##  tz       America/Los_Angeles         
##  date     2021-07-27                  
## 
## - Packages ----------------------------------------------------------------------------------------------
##  ! package     * version date       lib source                                 
##  P assertthat    0.2.1   2019-03-21 [?] CRAN (R 4.1.0)                         
##  P backports     1.2.1   2020-12-09 [?] CRAN (R 4.1.0)                         
##  P broom         0.7.8   2021-06-24 [?] CRAN (R 4.1.0)                         
##  P cachem        1.0.5   2021-05-15 [?] CRAN (R 4.1.0)                         
##  P callr         3.7.0   2021-04-20 [?] CRAN (R 4.1.0)                         
##  P cellranger    1.1.0   2016-07-27 [?] CRAN (R 4.1.0)                         
##  P cli           3.0.0   2021-06-30 [?] CRAN (R 4.1.0)                         
##  P cluster       2.1.2   2021-04-17 [?] CRAN (R 4.1.0)                         
##  P codetools     0.2-18  2020-11-04 [?] CRAN (R 4.1.0)                         
##  P colorspace    2.0-2   2021-06-24 [?] CRAN (R 4.1.0)                         
##  P crayon        1.4.1   2021-02-08 [?] CRAN (R 4.1.0)                         
##  P DBI           1.1.1   2021-01-15 [?] CRAN (R 4.1.0)                         
##  P dbplyr        2.1.1   2021-04-06 [?] CRAN (R 4.1.0)                         
##  P desc          1.3.0   2021-03-05 [?] CRAN (R 4.1.0)                         
##  P devtools      2.4.2   2021-06-07 [?] CRAN (R 4.1.0)                         
##  P digest        0.6.27  2020-10-24 [?] CRAN (R 4.1.0)                         
##  P dotCall64     1.0-1   2021-02-11 [?] CRAN (R 4.1.0)                         
##  P dplyr       * 1.0.7   2021-06-18 [?] CRAN (R 4.1.0)                         
##  P ellipsis      0.3.2   2021-04-29 [?] CRAN (R 4.1.0)                         
##  P evaluate      0.14    2019-05-28 [?] CRAN (R 4.1.0)                         
##  P fansi         0.5.0   2021-05-25 [?] CRAN (R 4.1.0)                         
##  P farver        2.1.0   2021-02-28 [?] CRAN (R 4.1.0)                         
##  P fastmap       1.1.0   2021-01-25 [?] CRAN (R 4.1.0)                         
##  P fields        12.5    2021-06-25 [?] CRAN (R 4.1.0)                         
##  P forcats     * 0.5.1   2021-01-27 [?] CRAN (R 4.1.0)                         
##  P fs            1.5.0   2020-07-31 [?] CRAN (R 4.1.0)                         
##  P generics      0.1.0   2020-10-31 [?] CRAN (R 4.1.0)                         
##  P ggplot2     * 3.3.5   2021-06-25 [?] CRAN (R 4.1.0)                         
##  P glue          1.4.2   2020-08-27 [?] CRAN (R 4.1.0)                         
##  P goeveg      * 0.5.1   2021-05-10 [?] CRAN (R 4.1.0)                         
##  P gridExtra     2.3     2017-09-09 [?] CRAN (R 4.1.0)                         
##  P gtable        0.3.0   2019-03-25 [?] CRAN (R 4.1.0)                         
##  P haven         2.4.1   2021-04-23 [?] CRAN (R 4.1.0)                         
##  P highr         0.9     2021-04-16 [?] CRAN (R 4.1.0)                         
##  P hms           1.1.0   2021-05-17 [?] CRAN (R 4.1.0)                         
##  P htmltools     0.5.1.1 2021-01-22 [?] CRAN (R 4.1.0)                         
##  P httr          1.4.2   2020-07-20 [?] CRAN (R 4.1.0)                         
##  P jsonlite      1.7.2   2020-12-09 [?] CRAN (R 4.1.0)                         
##  P katereR       0.1.0   2021-07-15 [?] Github (katekathrynkat/katereR@a771b5e)
##  P knitr         1.33    2021-04-24 [?] CRAN (R 4.1.0)                         
##  P labeling      0.4.2   2020-10-20 [?] CRAN (R 4.1.0)                         
##  P lattice     * 0.20-44 2021-05-02 [?] CRAN (R 4.1.0)                         
##  P lifecycle     1.0.0   2021-02-15 [?] CRAN (R 4.1.0)                         
##  P lubridate   * 1.7.10  2021-02-26 [?] CRAN (R 4.1.0)                         
##  P magrittr      2.0.1   2020-11-17 [?] CRAN (R 4.1.0)                         
##  P maps          3.3.0   2018-04-03 [?] CRAN (R 4.1.0)                         
##  P MASS          7.3-54  2021-05-03 [?] CRAN (R 4.1.0)                         
##  P Matrix        1.3-3   2021-05-04 [?] CRAN (R 4.1.0)                         
##  P memoise       2.0.0   2021-01-26 [?] CRAN (R 4.1.0)                         
##  P mgcv          1.8-35  2021-04-18 [?] CRAN (R 4.1.0)                         
##  P modelr        0.1.8   2020-05-19 [?] CRAN (R 4.1.0)                         
##  P munsell       0.5.0   2018-06-12 [?] CRAN (R 4.1.0)                         
##  P nlme          3.1-152 2021-02-04 [?] CRAN (R 4.1.0)                         
##  P permute     * 0.9-5   2019-03-12 [?] CRAN (R 4.1.0)                         
##  P pillar        1.6.1   2021-05-16 [?] CRAN (R 4.1.0)                         
##  P pkgbuild      1.2.0   2020-12-15 [?] CRAN (R 4.1.0)                         
##  P pkgconfig     2.0.3   2019-09-22 [?] CRAN (R 4.1.0)                         
##  P pkgload       1.2.1   2021-04-06 [?] CRAN (R 4.1.0)                         
##  P prettyunits   1.1.1   2020-01-24 [?] CRAN (R 4.1.0)                         
##  P processx      3.5.2   2021-04-30 [?] CRAN (R 4.1.0)                         
##  P ps            1.6.0   2021-02-28 [?] CRAN (R 4.1.0)                         
##  P purrr       * 0.3.4   2020-04-17 [?] CRAN (R 4.1.0)                         
##  P R6            2.5.0   2020-10-28 [?] CRAN (R 4.1.0)                         
##  P Rcpp          1.0.6   2021-01-15 [?] CRAN (R 4.1.0)                         
##  P readr       * 1.4.0   2020-10-05 [?] CRAN (R 4.1.0)                         
##  P readxl        1.3.1   2019-03-13 [?] CRAN (R 4.1.0)                         
##  P remotes       2.4.0   2021-06-02 [?] CRAN (R 4.1.0)                         
##    renv          0.13.2  2021-03-30 [1] CRAN (R 4.1.0)                         
##  P reprex        2.0.0   2021-04-02 [?] CRAN (R 4.1.0)                         
##  P rlang         0.4.11  2021-04-30 [?] CRAN (R 4.1.0)                         
##  P rmarkdown     2.9     2021-06-15 [?] CRAN (R 4.1.0)                         
##  P rprojroot     2.0.2   2020-11-15 [?] CRAN (R 4.1.0)                         
##  P rstudioapi    0.13    2020-11-12 [?] CRAN (R 4.1.0)                         
##  P rvest         1.0.0   2021-03-09 [?] CRAN (R 4.1.0)                         
##  P scales        1.1.1   2020-05-11 [?] CRAN (R 4.1.0)                         
##  P sessioninfo   1.1.1   2018-11-05 [?] CRAN (R 4.1.0)                         
##  P spam          2.7-0   2021-06-25 [?] CRAN (R 4.1.0)                         
##  P stringi       1.6.2   2021-05-17 [?] CRAN (R 4.1.0)                         
##  P stringr     * 1.4.0   2019-02-10 [?] CRAN (R 4.1.0)                         
##  P testthat      3.0.4   2021-07-01 [?] CRAN (R 4.1.0)                         
##  P tibble      * 3.1.2   2021-05-16 [?] CRAN (R 4.1.0)                         
##  P tidyr       * 1.1.3   2021-03-03 [?] CRAN (R 4.1.0)                         
##  P tidyselect    1.1.1   2021-04-30 [?] CRAN (R 4.1.0)                         
##  P tidyverse   * 1.3.1   2021-04-15 [?] CRAN (R 4.1.0)                         
##  P usethis       2.0.1   2021-02-10 [?] CRAN (R 4.1.0)                         
##  P utf8          1.2.1   2021-03-12 [?] CRAN (R 4.1.0)                         
##  P vctrs         0.3.8   2021-04-29 [?] CRAN (R 4.1.0)                         
##  P vegan       * 2.5-7   2020-11-28 [?] CRAN (R 4.1.0)                         
##  P viridis       0.6.1   2021-05-11 [?] CRAN (R 4.1.0)                         
##  P viridisLite   0.4.0   2021-04-13 [?] CRAN (R 4.1.0)                         
##  P withr         2.4.2   2021-04-18 [?] CRAN (R 4.1.0)                         
##  P xfun          0.24    2021-06-15 [?] CRAN (R 4.1.0)                         
##  P xml2          1.3.2   2020-04-23 [?] CRAN (R 4.1.0)                         
##  P yaml          2.2.1   2020-02-01 [?] CRAN (R 4.1.0)                         
## 
## [1] C:/Users/kathr/Documents/git-repos/lizard-guts-naxos/renv/library/R-4.1/i386-w64-mingw32
## [2] C:/Users/kathr/AppData/Local/Temp/RtmpWykWok/renv-system-library
## 
##  P -- Loaded and on-disk path mismatch.